[med-svn] [Git][med-team/kmc][master] 4 commits: simde patch: fixup badly ordered #elif.

Étienne Mollier (@emollier) gitlab at salsa.debian.org
Mon Jul 17 11:45:28 BST 2023 


Étienne Mollier pushed to branch master at Debian Med / kmc


Commits:
c76c00c2 by Étienne Mollier at 2023-07-17T11:35:30+02:00
simde patch: fixup badly ordered #elif.

The correction required a refresh of support-mixed-march.patch.

Gbp-Dch: ignore

- - - - -
5263589f by Étienne Mollier at 2023-07-17T12:33:29+02:00
makefile.patch: link dynamically binaries.

That is probably the last fixup to get kmc back in decent shape.

Gbp-Dch: ignore

- - - - -
f1733004 by Étienne Mollier at 2023-07-17T12:34:42+02:00
gcc-13.patch: new: fix build failures with gcc-13.

Closes: #1037708

- - - - -
c995e385 by Étienne Mollier at 2023-07-17T12:44:36+02:00
ready to upload to unstable.

- - - - -


6 changed files:

- debian/changelog
- + debian/patches/gcc-13.patch
- debian/patches/makefile.patch
- debian/patches/series
- debian/patches/simde
- debian/patches/support-mixed-march.patch


Changes:

=====================================
debian/changelog
=====================================
@@ -1,4 +1,4 @@
-kmc (3.2.2+dfsg-1) UNRELEASED; urgency=medium
+kmc (3.2.2+dfsg-1) unstable; urgency=medium
 
   * New upstream version
   * Standards-Version: 4.6.2 (routine-update)
@@ -8,8 +8,9 @@ kmc (3.2.2+dfsg-1) UNRELEASED; urgency=medium
   * disable-python-bindings.patch: refresh.
   * simde patch: refresh.
   * support-mixed-march.patch: refresh.
+  * gcc-13.patch: new: fix build failures with gcc-13. (Closes: #1037708)
 
- -- Étienne Mollier <emollier at debian.org>  Mon, 17 Jul 2023 11:06:02 +0200
+ -- Étienne Mollier <emollier at debian.org>  Mon, 17 Jul 2023 12:35:26 +0200
 
 kmc (3.2.1+dfsg-1) unstable; urgency=medium
 


=====================================
debian/patches/gcc-13.patch
=====================================
@@ -0,0 +1,41 @@
+Description: fix ftbfs with gcc-13
+Author: Étienne Mollier <emollier at debian.org>
+Bug-Debian: https://bugs.debian.org/1037708
+Forwarded: no
+Last-Update: 2023-07-17
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- kmc.orig/kmc_core/critical_error_handler.h
++++ kmc/kmc_core/critical_error_handler.h
+@@ -1,6 +1,7 @@
+ #pragma once
+ 
+ #include <set>
++#include <stdexcept>
+ #include <mutex>
+ #include "thread_cancellation_exception.h" //TODO: moze ten wyjatek zdefiniowac tutaj?
+ #include <condition_variable>
+--- kmc.orig/kmc_core/kff_writer.h
++++ kmc/kmc_core/kff_writer.h
+@@ -1,5 +1,6 @@
+ #pragma once
+ 
++#include <cstdint>
+ #include <string>
+ #include <vector>
+ 
+@@ -49,4 +50,4 @@
+ 	void FinishSection();
+ 
+ 	~CKFFWriter();
+-};
+\ No newline at end of file
++};
+--- kmc.orig/kmc_tools/kff_info_reader.h
++++ kmc/kmc_tools/kff_info_reader.h
+@@ -1,4 +1,5 @@
+ #pragma once
++#include <cstdint>
+ #include <string>
+ #include <vector>
+ #include <limits>


=====================================
debian/patches/makefile.patch
=====================================
@@ -8,15 +8,19 @@ Forwarded: not-needed
 
 --- kmc.orig/Makefile
 +++ kmc/Makefile
-@@ -67,7 +67,7 @@
+@@ -66,9 +66,9 @@
+ 	PY_FLAGS = -fPIC
  endif
  
- 
+-
 -CFLAGS	= -Wall -O3 -fsigned-char $(CPU_FLAGS) $(STATIC_CFLAGS) -std=c++14
-+CXXFLAGS+= -Wall -O3 -fsigned-char $(STATIC_CFLAGS) -std=c++14
- CLINK	= -lm $(STATIC_LFLAGS) -O3 -std=c++14
+-CLINK	= -lm $(STATIC_LFLAGS) -O3 -std=c++14
++LIB_ZLIB = -lz
++CXXFLAGS+= -Wall -O3 -fsigned-char -std=c++14
++CLINK	= -lm -O3 -std=c++14 -lz
  PY_KMC_API_CFLAGS = $(PY_FLAGS) -Wall -shared -std=c++14 -O3
  
+ KMC_CLI_OBJS = \
 @@ -143,19 +143,19 @@
  
  
@@ -43,9 +47,12 @@ Forwarded: not-needed
  
  
  $(LIB_KMC_CORE): $(KMC_CORE_OBJS) $(RADULS_OBJS) $(KMC_API_OBJS) $(KFF_OBJS)
-@@ -166,22 +166,22 @@
+@@ -164,24 +164,24 @@
+ 	-mkdir -p $(OUT_BIN_DIR)
+ 	ar rcs $@ $^
  
- kmc: $(KMC_CLI_OBJS) $(LIB_KMC_CORE) $(LIB_ZLIB)
+-kmc: $(KMC_CLI_OBJS) $(LIB_KMC_CORE) $(LIB_ZLIB)
++kmc: $(KMC_CLI_OBJS) $(LIB_KMC_CORE)
  	-mkdir -p $(OUT_BIN_DIR)
 -	$(CC) $(CLINK) -o $(OUT_BIN_DIR)/$@ $^ $(LIB_ZLIB)
 +	$(CXX) $(CPPFLAGS) $(CXXFLAGS) $(CLINK) -o $(OUT_BIN_DIR)/$@ $^ $(LIB_ZLIB)
@@ -55,7 +62,8 @@ Forwarded: not-needed
 -	$(CC) $(CLINK) -o $(OUT_BIN_DIR)/$@ $^
 +	$(CXX) $(CPPFLAGS) $(CXXFLAGS) $(CLINK) -o $(OUT_BIN_DIR)/$@ $^
  
- kmc_tools: $(KMC_TOOLS_OBJS) $(KMC_API_OBJS) $(KFF_OBJS) $(LIB_ZLIB)
+-kmc_tools: $(KMC_TOOLS_OBJS) $(KMC_API_OBJS) $(KFF_OBJS) $(LIB_ZLIB)
++kmc_tools: $(KMC_TOOLS_OBJS) $(KMC_API_OBJS) $(KFF_OBJS)
  	-mkdir -p $(OUT_BIN_DIR)
 -	$(CC) $(CLINK) -I 3rd_party/cloudflare -o $(OUT_BIN_DIR)/$@ $^ $(LIB_ZLIB)
 +	$(CXX) $(CPPFLAGS) $(CXXFLAGS) $(CLINK) -o $(OUT_BIN_DIR)/$@ $^ $(LIB_ZLIB)


=====================================
debian/patches/series
=====================================
@@ -5,3 +5,4 @@ disable-python-bindings.patch
 spelling.patch
 simde
 support-mixed-march.patch
+gcc-13.patch


=====================================
debian/patches/simde
=====================================
@@ -157,15 +157,19 @@ Description: support non-x86 systems via libsimde-dev
 +// ***** EOF
 --- kmc.orig/kmc_core/raduls_impl.h
 +++ kmc/kmc_core/raduls_impl.h
-@@ -759,7 +759,7 @@
+@@ -759,10 +759,10 @@
  #define RADULS_RADIX_SORT_FUNNAME RadixSortMSD_AVX
  #elif defined(__SSE4_1__)
  #define RADULS_RADIX_SORT_FUNNAME RadixSortMSD_SSE41
 -#elif defined(__SSE2__)
-+#else
- #define RADULS_RADIX_SORT_FUNNAME RadixSortMSD_SSE2
+-#define RADULS_RADIX_SORT_FUNNAME RadixSortMSD_SSE2
  #elif defined(__aarch64__)
  #define RADULS_RADIX_SORT_FUNNAME RadixSortMSD_NEON
++#else
++#define RADULS_RADIX_SORT_FUNNAME RadixSortMSD_SSE2
+ #endif
+ 
+ 
 @@ -800,4 +800,4 @@
  
  #endif


=====================================
debian/patches/support-mixed-march.patch
=====================================
@@ -26,7 +26,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
  // ***** EOF
 --- kmc.orig/kmc_core/raduls_impl.h
 +++ kmc/kmc_core/raduls_impl.h
-@@ -754,12 +754,20 @@
+@@ -754,14 +754,19 @@
  	}
  
  #if defined(__AVX2__)
@@ -38,15 +38,14 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
  #elif defined(__SSE4_1__)
 +#warning "building raduls radix sort for sse4.1"
  #define RADULS_RADIX_SORT_FUNNAME RadixSortMSD_SSE41
+ #elif defined(__aarch64__)
++#warning "building raduls radix sort for neon"
+ #define RADULS_RADIX_SORT_FUNNAME RadixSortMSD_NEON
  #else
-+#if defined(__SSE2__)
 +#warning "building raduls radix sort for sse2"
-+#else
-+#warning "building raduls radix sort for debian baseline with simde sse2 compat"
-+#endif
  #define RADULS_RADIX_SORT_FUNNAME RadixSortMSD_SSE2
- #elif defined(__aarch64__)
- #define RADULS_RADIX_SORT_FUNNAME RadixSortMSD_NEON
+ #endif
+ 
 --- kmc.orig/kmc_core/raduls_sse2.cpp
 +++ kmc/kmc_core/raduls_sse2.cpp
 @@ -8,6 +8,15 @@



View it on GitLab: https://salsa.debian.org/med-team/kmc/-/compare/b80a4bb1aad615cdd24477a1e50df34c65c816ad...c995e38571f728ded0e18e49d8d4f0bd966f3f90

-- 
View it on GitLab: https://salsa.debian.org/med-team/kmc/-/compare/b80a4bb1aad615cdd24477a1e50df34c65c816ad...c995e38571f728ded0e18e49d8d4f0bd966f3f90
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